👷 Run CI (lint, tests) on Github Workflows

.github/workflows/ci.yml

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+
+name: ✅ CI 
+
+on:
+  pull_request:
+    types: [opened, reopened, edited, synchronize, closed] 
+
+concurrency:
+  group: ci-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    runs-on: ubuntu-20.04
+    timeout-minutes: 10
+    steps:
+      - name: 👩‍💻 Checkout code
+        uses: actions/checkout@v3
+
+      - name: 🐍 Setup Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.8'
+
+      - name: 📦 Install deps
+        run: |
+          pip install black 
+
+      - name: 🚨 Lint code 
+        run: |
+          black --check --line-length 80 kf_update_dbgap_consent tests
+
+  test:
+    runs-on: ubuntu-20.04
+    timeout-minutes: 10
+    steps:
+      - name: 👩‍💻 Checkout code
+        uses: actions/checkout@v3
+
+      - name: 🐳 Start Dataservice docker-compose
+        run: |
+          ./bin/setup_dataservice.sh
+
+      - name: 🐍 Setup Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.8'
+
+      - name: 📦 Install deps
+        run: |
+          pip install --upgrade virtualenv
+          virtualenv -p python3 venv
+          source venv/bin/activate
+          pip install -r dev-requirements.txt
+          pip install -e .
+
+      - name: ✅ Test
+        run: |
+          source venv/bin/activate
+          pytest tests
+

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+### Ingest stuff
+cached_schema.json
+*.tsv
+*.csv
+*.xls
+*.xlsx
+*.txt
+
+# Ingest outputs
+kf_ingest_packages/packages/**/output/*
+
+# Exclude uid cache db
+!kf_ingest_packages/packages/**/output/*.db
+
+# Exclude count analysis report
+!kf_ingest_packages/packages/**/counts*.log
+
+# Exclude ingest logs
+!kf_ingest_packages/packages/**/ingest*.log
+
+# dot files and folders
+.*
+
+# Exclude github workflows
+!/.github
+
+# Exclude validation test results
+!kf_ingest_packages/packages/**/validation_results/*
+
+# Validation Report Site
+## Build dir
+web/site
+
+# CI Artifacts
+kf-api-dataservice

bin/health-check.sh

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+#!/bin/bash
+
+# Dataservice Health Check 
+
+set -e
+
+START_TIME=$SECONDS
+DATASERVICE_ENDPOINT=${DATASERVICE_ENDPOINT:-http://localhost:5000}
+
+echo "⛑️ Waiting for service to become healthy ..."
+until $(curl --output /dev/null --head --silent --fail $DATASERVICE_ENDPOINT/status)
+do
+    echo -n "."
+    sleep 2
+done
+
+ELAPSED=$((( SECONDS - START_TIME ) / 60 ))
+FORMATTED_ELAPSED=$(printf "%.2f" $ELAPSED)
+echo ""
+echo "Elapsed time $FORMATTED_ELAPSED minutes"
+
+echo "✅ --- Development environment setup complete! ---"
+

bin/setup_dataservice.sh

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+#!/bin/bash
+
+# Dataservice Setup 
+
+set -e
+
+if [ -d "./kf-api-dataservice" ];
+then
+    cd kf-api-dataservice
+    git pull
+    cd ..
+else
+    git clone --depth 1 https://github.com/kids-first/kf-api-dataservice.git
+fi
+cp kf-api-dataservice/.env.sample kf-api-dataservice/.env
+cp docker-compose.yml kf-api-dataservice/
+docker-compose -f kf-api-dataservice/docker-compose.yml up -d --build
+./bin/health-check.sh

docker-compose.yml

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+version: '3'
+
+services:
+  dataservice_pg:
+    container_name: dataservice_pg
+    image: postgres:11.1
+    env_file:
+      - .env
+    environment:
+      POSTGRES_DB: "${DATASERVICE_DB}"
+      POSTGRES_USER: "${DATASERVICE_DB_USER}"
+      POSTGRES_PASSWORD: "${DATASERVICE_DB_PASSWORD}"
+    ports:
+        - "5432:5432"
+  dataservice:
+    container_name: dataservice
+    build: 
+      context: .
+      target: test
+    command: /bin/ash -c "sleep 5; ./bin/run.sh"
+    volumes:
+      - .:/app
+    ports:
+      - "5000:80"
+    env_file:
+      - .env
+    environment:
+      FLASK_CONFIG: "${FLASK_CONFIG}"
+      FLASK_APP: "${FLASK_APP}"
+      PG_HOST: "${DATASERVICE_PG_HOST}"
+      PG_PORT: "${DATASERVICE_PG_PORT}"
+      PG_NAME: "${DATASERVICE_DB}"
+      PG_USER: "${DATASERVICE_DB_USER}"
+      PG_PASS: "${DATASERVICE_DB_PASSWORD}"
+    depends_on:
+      - dataservice_pg